<div id="result">
    <form id="taxForm" name="taxForm">
        <fieldset title='Input section' style="padding-left: 5px">    
            <legend>Input</legend>
            <br>
            Full path to input file (reads):
            <font title="Check for fasta input">
            &nbsp;&nbsp;&nbsp;&nbsp; Is the input fasta?</font>
            <input id='fasta' type="checkbox" title="Check for fasta input"/>
            <br>
            <input id='seq' size="80"/>        
            <br>
            Full path to output directory:
            <font title="Check for megan output">
            &nbsp;&nbsp;&nbsp;&nbsp; Check for megan output </font>
            <input id='megan' type="checkbox" title="Check for megan output"/>
            <br>
            <input id='o' size="80"/><br>
            <table>
                <tr style="background: none;">
                    <td>Database to be used during the alignment:</td>
                </tr>
                <tr style="background: none;">
                    <td>
                        <select id = "dbList" multiple="multiple" required="required" size="7" onclick="verifyDBList(this.form)" >
                            <option value = "0" title="Select to use all databases">All</option>
                            <option value = "1" selected="selected" title="Bacteria database">Bacteria</option>
                            <option value = "2" title="Archaea database">Archaea</option>
                            <option value = "3" title="Viruses database">Viruses</option>
                            <option value = "4" title="Fungi database">Fungi</option>
                            <option value = "5" title="Select to set your own database">Other</option>
                        </select>
                    </td>
                    <td>
                        <div id="otherDB">                            
                        </div>                        
                    </td>
                </tr>                 
            </table>
            Path to nodes.dmp file from NCBI Taxonomy database:<br>
            <input id='taxpath' size="80" value="databases/nodes.dmp"/>
        </fieldset>  
        <fieldset title='Input section' style="padding-left: 5px">
            <legend>Optional inputs</legend>
            <br> 
            <div align="center">
                <font title="Align reads against host, and remove host reads">
                No filter by host:</font>
                <input id='nohostfilter' type="checkbox" title="Align reads against host, and remove host reads"/>&nbsp;&nbsp;&nbsp;&nbsp;
                <font title="Max hits searched for each read during alignment (def: 10)">Max hits:</font>  
                <input id='bt2maxhits' size="2" value="10" title="Max hits searched for each read during alignment (def: 10)"/>&nbsp;&nbsp;&nbsp;&nbsp;
                <font title="Alignment score (0.001 - 1)">Score:</font>   
                <input id='neighborscore' size="3" value="0.99" title="Alignment score (0.001 - 1)"/><br>
                <font title="Get all valid alignments with bowtie2">All alignments:</font>  
                <input id='bt2allhits' type="checkbox" title="Get all valid alignments with bowtie2"/> &nbsp;&nbsp;&nbsp;&nbsp;
                <font title="Redo nearest neighbor search for alignment files in the specified output folder">Do not realign:</font>  
                <input id='onlyneighbor' type="checkbox" title="Redo nearest neighbor search for alignment files in the specified output folder"/>&nbsp;&nbsp;&nbsp;&nbsp;
                <font title="1 thread per 8GB of RAM">Number of threads:</font> 
                <input id='p' size="2" value="1" title="1 thread per 8GB of RAM"/>
            </div>            
            <font title="If the reads are sequenced in paired-end mode, you can specify the second pair file">
            Full path to second pair file:
            </font>
            <input id='paired' size="80"/>
            <br>
            <font title="Minimum insert size for paired-end (default 0)">Minimum insert size for paired-end:</font>   
            <input id='I' size="3" value="0" title="Minimum insert size for paired-end (default 0)"/>&nbsp;&nbsp;&nbsp;&nbsp;
            <font title="Maximum insert size for paired-end (default 500)">Maximum insert size for paired-end:</font>   
            <input id='X' size="3" value="500" title="Maximum insert size for paired-end (default 500)"/>
            <br>
            <b>Note:</b> If paired-end mode is chosen, host filtering is disabled, and bowtie2 is used with --no-mixed and --no-discordant (reads have to be concordant, and both read pairs have to align).
        </fieldset>  
        <div class='required' id='submit' >
            <input  type="button" value="Run!" onclick='JavaScript:xmlhttpUpload("http://127.0.0.1:8083/?cmd=./bin/taxoner", "taxForm", "0")'>
            <input type='reset' />
        </div>
    </form>
</div>

